Finding the Commander
by Jpcthunder
Summary: The Reapers are gone, destroyed by Commander Shepard. The Crucible was destroyed as well, but the Commander's body was never found. Refusing to believe he is dead, the crew of the SSV Normandy, led by Garrus Vakarian and Miranda Lawson, set out to find him. Little do they know, Shepard is in the hands of a cruel general, being tortured in his arena. Can the crew find him in time?
1. Strings

**Chapter 1: Strings**

_SSV Normandy SR2 (reconstructed)_

_November 24__th__ 2189_

_Christmas Eve, almost four years after destruction of the Reapers_

"Just drink it Garrus" Urdnot Grunt snapped at the turian.

"You told me it could poison me" Garrus Vakarian snapped back as Grunt cracked his fingers and readjusted his armor plating.

"Well then hurry up and poison yourself already." His krogan squad mate growled "Or I'll drink it myself."

"You'd poison your captain" Garrus asked.

The two soldiers sat at the SSV Normandy's lounge, bickering over a glass of Krogan liquor. There had been many changes to the Normandy as of late. In the absence of the former commanding officer, Garrus had been promoted to captain the Normandy in his stead. Along with the positional changes, modifications had been made to the ship after its reconstruction. The Normandy Lounge was the newest and previously most requested section of the rebuilt frigate. A large circular bar sat in the middle of the large room. Large bottles of Asari, Turian, Krogan, and Human liquors, wines, and spirits lined the shelves and were scattered across the bar. The lounge was designed to provide comfort for all of the species on board. Large, hefty chairs with stiff cushions for krogans like Grunt. Tall chairs with less smooth wood for the tough skin of turians like Garrus, as well as booths with comfortable cushions for the asari and humans aboard.

"Careful, Grunt" Jeff 'Joker' Moreau told his krogan friend. "You don't want him to start beating you…"

"…With the stick up my ass" Garrus rolled his eyes "You realize that joke has lost its value, right?"

"It's better than all the material you got." Joker said as he swallowed down a glass of beer.

"Shouldn't you be flying the ship, Joker?" Grunt asked, agitated that his good time of messing with Garrus was interrupted.

"EDI's got it" he said, "She can operate autopilot and be here at the same time." Joker wrapped his arm around his robotic companion.

"Due to my faster reaction time and accessibility to the Normandy's cannons and shield technology, I can pilot the ship 13 percent more efficiently than Joker." The AI gloated and smirked a synthetic smile.

"Is there anything in your programming that involves modesty?" a new voice asked as a new person entered the conversation.

"Actually, Dr. T'Soni" EDI started "Perhaps you could inform me as to how it works."

Liara grabbed a bottle of an asari spirit and opened it, pouring the green liquid into the glass in front of her. "Can we for once talk about something that doesn't involve a mission or weapons or the ship?"

"What else is there to talk about?" Grunt asked aggravated.

"Yeah" Garrus said "I never thought I'd say it, but Grunt is right." The krogan next to him growled. "This party is a distraction, there's a reason this ship is in space right now and not in an Alliance museum."

"Oh please" Liara said "The SSV Mississippi is the only Alliance frigate that can actually outpace the Normandy. Oh damn it now I'm doing it now."

"Hey hey hey, Liara" Joker stopped and set down his drink. "There is not one ship in the galaxy that can outpace the Normandy on her worst day." He said "and there is no way I'm letting my baby ever be put in a museum."

"I agree with Joker" Garrus said "This ship is still the best of the best."

Liara let out a small chuckle "You're only saying that because the Turians helped design it."

"We helped with plenty of other things on this ship too" Garrus said.

"Oh yeah" Liara asked "Like what?"

"Ugh…" Garrus stammered "Calibrations"

The group erupted in laughter as James Vega, Dr. Karin Chakwas and Samantha Traynor entered the lounge. Joker poured several shots as the rest of the Normandy's crew piled in. "Is this everyone?" he looked around and set the shots down on a tray. "No, we're missing somebody." Joker walked past James as he flexed a muscle for the growing crowd. "Hey EDI" Joker addressed the AI.

"Joker?" she turned away from Liara and Dr. Chakwas.

"Can you run a scan of the ship, we're missing our XO"

"Of course" the process took less than three seconds. "Our Executive Officer is on the CIC"

"Ok, I'll go up there and inform the XO of the Christmas party brewing."

Joker walked up the small staircase slowly. Garrus chose to join him up to the CIC in the elevator, using this as the chance to escape from the Urdnot clansman still trying to poison him. Joker and Garrus entered the elevator.

"She doesn't seem right" Joker said to Garrus as they rode the elevator up to the CIC.

"What?" Garrus asked, obviously slightly buzzed. "Who?"

"The woman we're going to get you idiot." Joker chuckled "You're second in command."

"Right" he said "Right, I remember now" he hiccupped as they exited the elevator and entered the CIC.

Miranda Lawson was standing at the galaxy map platform, sweeping her hand across the holographic surface that displayed the stars and planets of the Milky Way. She was wearing the same outfit she always did, the same tight white suit that hung to her perfectly. "Joker, Garrus" she didn't turn to them as she shuffled through the map.

Joker leaned against a console to take the pressure off his brittle legs. "I still remember when you were calling me 'Mr. Moreau'"

"I was a little more formal back then." She said as she highlighted a planet on the map. "What do you think about Minos Wasteland?"

"Not sure" Garrus said "Could be, probably not."

"Dirada then, that was my second choice for the next mission."

Joker exhaled softly "Look, Miranda, there's a big Christmas party going on in the lounge right now." He scratched at his beard "Maybe you should come downstairs and have a cocktail or something."

"I'm working Joker" she said sternly as she typed on the laptop beside her, propped up on another desk.

Garrus crossed his arms "Miranda, take the night off."

"Do turians even celebrate Christmas?" Miranda asked as she turned, her hair whipped around as she faced the Palaven born soldier.

"It's a purely human tradition," Garrus said "But, nonetheless, an excuse to take some time off."

"It seems like I'm the only one on this ship focused right now." She turned back towards the holographic display "The rest of you can drink your silly little drinks and open your silly little presents, while I look for the REAL Commander of the Normandy."

"Garrus is a great captain, Miranda" Joker said as he stepped off the control panel. "It's almost been four years…"

Miranda turned around again. "I knew it" she said as she pushed a finger into the pilot's chest. "I knew you people would eventually give up!"

"Nobody is giving up Miranda" Garrus said "All Joker was saying is that you need to calm down, take it slow, and relax before you drive yourself crazy."

"You wanna see crazy" Miranda snapped at the turian. The former Cerberus officer looked as if she was about to let loose on Garrus with a biotic attack. Joker grabbed the back of her arm. Miranda's intense glare wavered slightly, and a small teardrop ran down her cheek. She fell onto the floor and sobbed. Garrus knelt down next to her and held a hand on her shoulder. "I know how much you love him. Wherever he is, we know he's alive. He disappeared after the Crucible."The turian said as they sat there.

"I know you don't think so" Garrus said "But I miss him too."

* * *

_Four years ago_

"How long do you think you can hold out Commander?" a small distant voice said.

The Spectre thought before responding "As long as I need to."

"They won't let you rest for very long" the voice said "They're going to break you eventually, like they've broken all the others"

"I won't let them" He said as he ran a hand through his hair, the large metal chains rattled as he did so. "I'm unbreakable." There was a foul smell in the air, it smelled like rotting flesh.

The salarian to his right, chained up in the same manner he was, the same salarian he had been talking to for the past few hours. The alien chuckled "That's what everyone who comes through here says."

"How long has it been?"

"What do you mean?"

"I'm sure word has reached about the Crucible by now." Shepard struggled for breath in the damp stone chamber. "How long has it been since Earth, hours, months, years?"

"It's been a week, Commander. Just over seven days." Shepard could barely see the salarian shrug his shoulders. "Nowhere near as long as your last excursion"

"I'm just glad I haven't been out for another two years."

"I've been here for seven months. Or at least I think it's been seven months. It could be seven years for all I know" he rubbed his own bald head. "Hard to tell when you don't see sunlight pass."

"What is it like out there?" Shepard asked hesitantly.

"You're a Spectre Shepard." He said "Nothing you haven't already seen. Then again, I've seen that asshole up there pull out a lot of tricks."

"Tell me more about this general."

"He's a turian, his name's Kryatt" the salarian said "I don't know his first name. He treats fighting like a drug, he gets high on it. He had rich parents and they left everything to him when they died. So he bought a small planet and had enough left to buy this godforsaken place where…"

The salarian was interrupted by the sound of a loud clattering. "SHEPARD" a loud voice screamed. A door screeched open and light streamed into the room. The contents of the room were revealed. Shepard squinted at the figure in the doorway. A huge krogan, clad in armor was standing in the door, casting a large shadow over Shepard. The commander looked into the other corner, where a rotting body sat. It was another human, obviously dead. It was missing a leg, the torn off limb was taken from below the knee. Dried blood stained the stone floor.

"SHEPARD!" The Krogan screamed at him again. "Time to meet the General."

Shepard was picked up and dragged outside, blindfolded and not allowed to walk himself. He couldn't tell what direction left or right was, he was too tired to think and his head pulsed with confusion. The opaque bag over his head kept him from noticing his surroundings.

He could hear the opening of a door, the telltale beep he had heard so many times. The commander was seated down in a chair, he felt around, it was wooden. He could feel a gun pressed against the back of his head. "You try anything, and my shotgun takes your head off."

"Yeah yeah" he said, more confidently than he should have. The Krogan grunted loudly and a sharp pain rang out through Shepard's head. The chair tipped over and the commander fell. The Krogan had hit him over the head with the shotgun barrel. He was put back in the chair and finally, the bag came off.

Shepard was treated with a sight of a turian. The only turian this could be, the General. "Commander Shepard" he said, "Systems Alliance veteran, Council Spectre. You are quite the famous soldier."

"Where am I?" Shepard asked

"My arena" the turian said as he swirled a glass of wine in his hand. "I own the planet. It's a small one, to be sure, but still a planet."

"What do you want from me?"

"You are a great soldier to be sure" the General said "But are you a warrior?"

"Why am I here?"

"I'm going to capitalize on you. You may have noticed the salarian in the cell with you. He was a decorated soldier from the STG" he took a sip from his glass of wine. "Now, he is nothing more than a puppet. You're a decorated soldier. I haven't decided what I'm going to do to you specifically."

"An arena?" Shepard asked "Your making me fight in an arena. When my crew finds me, you are going to a cell on the Citadel for war crimes, then executed."

"I was told you were very overconfident"

"By whom?" Shepard asked.

"Doesn't matter now" the General said "You're my puppet, and I hold all the strings."


	2. Customs

**Chapter 2: Customs**

Earth

In all her years of travel and galactic exploration, Miranda had never been on the human home world before. She'd seen it plenty of times from the upper atmosphere, or on a vid screen. She rested her arm against the window of the shuttle window and looked down at the waves as the Pacific pushed its way up the beach. Miranda had always wanted to go for vacation, to London or Paris, and experience everything she had read about in her books as a child. She wished that her and her friends were here for a vacation and not for a mission as important as this. She brushed her hand down the high cut leather jacket and white tee shirt she wore, and pushed her free hand into the pockets of her tight, blue denim jeans. Miranda shuffled her feet on her brown boots as she looked out the window.

Garrus had been to Earth however, on the mission with Shepard. He thought Earth's architecture was radically different from Palaven's, yet just as extraordinary. He admired human weapon's technology, excited to look for a new sniper rifle while on planet. He struggled in the turian civilian clothes he wore, uncomfortable in anything but combat armor. They had to wear regular clothes here, not wanting to draw any attention in body armor or tight white combat suits. Garrus saw Miranda leaning against the window, spacing out at the sight of the human city in front of them. He grabbed her shoulder "You okay?"

"Fine" the raven haired woman said "Fine, I'm just… admiring the view." She lied.

Garrus saw the lie before she uttered the words, she was thinking about Shepard. The Commander was the only thing she thought about. He was on the minds of many crew members on the Normandy. "Alright" Garrus nodded "So you said you had a contact here?"

"Yes," she swept her hair back and turned to face the turian. "Alex Turner, a black-markets dealer of weapons and body armor. He recently sent out a shipment to deep space."

"So?" Garrus asked "What's that got to do with us?"

"He didn't specify a buyer on the manifest" she turned back to the window as she typed on her Omni-tool, showing him the empty page. "He always specifies a buyer before sending anything out that far. He wouldn't take the risk of mercenaries intercepting a shipment, looking for a quick score and not knowing who their crossing."

"And you think this has something to do with Shepard?"

"Wherever Shepard is, he's being surrounded with weapons. Turner knows something about every weapon that goes into deep space. If our Commander is out that far, Turner can point us in the right direction."

"Sounds like a plan," Garrus nodded "Let's talk to the arms dealer." He walked up to the cockpit as the human flight tower hailed them. "This is Captain Garrus Vakarian on Shuttle 954S, requesting landing privileges." He said into the microphone and waited for a response.

It took a second, but then the radio came to life and a female voice came up "Granted, Captain Vakarian, you are cleared for landing. An Alliance representative will escort you to the processing center."

"Alliance representative?" Miranda asked.

Garrus shrugged his shoulder. "Why the escort?" he asked into the microphone.

The woman in the tower responded. "Your name was flagged as turian," she said, "You will be escorted to the processing chamber, or submit to search of your ship and eviction from the planet."

Garrus hissed as he left the terminal and walked back to Miranda. "Flagged as turian." He snapped as he sat back down.

"It's the upgraded security." Miranda said "Since the Reaper attack, Earth has been exceedingly wary of alien travelers."

"Ugh" he rubbed his cheek, where the large scar remained a reminder of his trip to Omega. "This is going to take all day."

They docked at the spaceport soon after and were met by the Alliance representative. "Captain Vakarian" the man walked up to Garrus cautiously and with a hand on his pistol. "We would like you to hand over your weapons."

Garrus walked off of the shuttle "No" he said plainly as he stepped onto the pavement of the landing surface and strutted over to the Alliance soldier, whom he easily towered over.

"That wasn't a question." The man began to draw his sidearm when Miranda walked off of the shuttle.

"What's going on here?" she asked, ready to hit the Marine with a biotic attack if he threatened Garrus.

"A human!" he took his hand off of the gun and stood up straighter "Sorry ma'am,"

"You should be apologizing to the Captain, corporal" she noted the rank on his jacket.

"Of course ma'am" he nodded at her "Sorry" he breathed out, almost in a whisper, to Garrus. "We're heading over to the processing center. Please step into the vehicle." He gestured to the transport ten feet away. The Marine turned and walked to the vehicle, looking up Miranda on his Omni-tool.

"Did he really call me ma'am?" Miranda asked Garrus, almost in shock.

"Well, everyone gets old at some point." He shrugged his shoulders.

"I'm thirty nine" she gasped in horror.

"I didn't realize the commander was into older women" Garrus joked, and immediately regretted it as Miranda smacked his arm.

"You arse" she scowled "Your dead when we get back onboard." She disregarded the fact she was talking to her commanding officer. Although she was only the Normandy's Executive Officer, she often took the helm of the missions they went on, leaving Garrus in the dust. The ranks didn't hold much weight, as the Normandy was no longer an Alliance vessel, and not in the military. They still kept the official ranks to hold some sense of normalcy. The Normandy was rebuilt using Commander Shepard's private funding, which was extensive and placed in the care of Miranda before the destruction of the Reapers. The staggering amount of credits was earned from years of Alliance service that were never spent.

The two piled into the transport with the Marine, who smiled at Miranda "Ma'am, welcome to Los Angeles." They sped off, moving away from their shuttle as it flew off back into space.

A large processing center came into view after a short three minute ride. A large building with huge glass windows. The Marine parked the transport and directed them inside. They were brought to another representative, this time behind a desk.

"I'll ask again Captain, what brings you to Earth?" the female asked while looking over their papers.

"I told you," Garrus lied "My ship needs repairs and restocking."

"And how is it that you, a turian, ended up with an Alliance frigate." The woman took off her glasses and stared at Garrus.

"It's not an Alliance ship anymore" he said, "It was retrofitted and ejected from the fleet, and after four years it needs repairs." He snapped and sighed.

"I'm sorry; we cannot permit you into the city." She said "We can however, allow Miss Lawson into the city." She pointed to Garrus's companion.

"Why, because I'm a turian?"

"No" she stammered and looked for something to say, "You… she… we… we don't."

The woman was relieved by a newcomer to the room. An Alliance uniform, decorated with more than enough commendations and metals. Gray hair and a large beard covered his head and face, and distinction radiated from him as he strutted in. "That's all Weston" he nodded to the Alliance rep.

"Aye sir." She stood and saluted, refusing to move.

Garrus turned to look at his savior and addressed him "Admiral Hackett." He said with the respect that the soldier deserved, but didn't shake his hand either.

"Vakarian" he nodded at the turian and pointed to the door. "My office, down the hall, five doors to the right."

Miranda followed Garrus as they walked to the Admiral's office in silence. "That's Admiral Hackett huh?" she asked.

"Yeah," he said "I don't think he particularly likes me that much, so try to be charming and we might just escape detainment."

She scoffed and shook her head, "We're getting into Los Angeles, one way or another, even if we have to shoot our way out of here."

Garrus took his turn to scoff and laugh as they rounded the corner and walked into Hackett's office. A large room with glass panels, reading out Alliance statistics, (Which were immediately turned off as Garrus and Miranda entered) news channels, and security camera feeds. A large mahogany desk sat in the middle of the room, with a cushy leather chair, and several computers and data pads lay out on the desk.

Hackett hit the button to shut the door behind him as he moved to his desk. "I don't believe we've met" he said to Miranda.

"I've heard of you many times, Admiral." Miranda said "The stories of you during the Reaper War have passed through my ears more than once. I'm Miranda Lawson, Executive Officer of the Normandy."

Hackett nodded and gestured for the two to take a seat across from him "Speaking of the Normandy, what is it doing in the lower atmosphere?" he asked Garrus grimly.

"It's my ship." He said, "Shepard's will made it clear that he wanted me to assume command of the frigate."

"Right," Hackett sighed "The same will that was read after the funeral you didn't go to."

Garrus sat back in his chair. "I don't go to funerals for men whom I know are alive."

"Excuse me?" Hackett sat up, in contrast to Garrus.

"You honestly think we're here for repairs and supplies" Miranda asked "We could have gone to the Citadel, better prices anyway."

Garrus gave her a look that said 'whatever happened to charming?' "We need to get into Los Angeles, Admiral."

Hackett took a large breath. "You're looking for a dead man, captain."

"We can't think like that" Garrus said. "We can't afford to."

"You should." Hackett said "You should focus on the future. No one could possibly want Shepard back more than me, but…"

Miranda interrupted him "No, there are people who want Shepard back more than you. Me for example." She crossed her arms, hiking up the leather jacket and reaffirming her point.

"What are you?" the Admiral asked, "His girlfriend?"

She stayed silent, letting Garrus take control of the conversation again. "Well yeah, kinda" he gestured towards Miranda with his head.

"I'm sorry" He said to the ex Cerberus officer. "I miss the Commander too; he was one of the best soldiers I ever knew."

"If you're really sorry, you'll let us into the city." Miranda said grimly and turned from the Admiral, walking out of the door and decided to wait in the hall.

Garrus looked back at Hackett. "It's been tough for her these past years." He told him, standing up and placing his hands on the desk. "She doesn't sleep, barely eats, focuses only on him." he walked around the desk, leaving nothing in between the two. "Even if Shepard isn't alive, she's not going to rest until she finds the body. Then we'll have another funeral, but until then, I have to help her, either for Shepard or in his memory, because that's what he would have wanted."

Hackett took a minute, rubbing his beard softly and scratching his head "I'll authorize you to enter the city, for a few days. Do what you need to do and get off planet." He handed Garrus two data pads, one with his information and one with Miranda's. "These will get you access to most checkpoints."

Garrus finally took Hackett's hand "Thank you." He said as the Admiral stood and nodded.

"Just don't start any trouble, Garrus, that's the last thing I need on my plate today."

"We're just going to meet someone and get out of the city" Garrus said, "Then we'll be gone and out of your hair."

"What do you want?" Hackett asked

Garrus walked out of the room. "I just want my best friend back."


End file.
